Rationalization of the reduction potentials within the series of the high potential iron-sulfur proteins

An analysis of the factors affecting reduction potentials within a series of high potential iron-sulfur proteins (HiPIP) has been performed by calculating the different contributions to the variation of electrostatic energy upon addition of one electron to the oxidized form of the protein. Molecular dynamics calculations were used to generate model structures of HiPIPs for which X-ray data are not available, starting from the known structures of highly homologous proteins. We have calculated and analyzed the contributions to the electrostatic energy deriving from the net charges present on the surface of the protein, the partial charges present on the uncharged residues, the polarizability of the protein atoms, the solvent dipoles and polarizabilities. A positive correlation with the reduction potentials was found only for the contribution due to the net charge of the protein which, in the absence of other factors such as differences in the coordination properties and in reorganizational energy upon reduction, is proposed to represent the determining effect for the large variation in reduction potential within this series of biological electron carriers.     

15N chemical shift changes in cytochrome b5: redox-dependent vs. guanidinium chloride-induced changes

The origin of the recently reported chemical shift changes of backbone amide nitrogens of redox proteins upon redox state changes has been investigated. These effects are particularly marked in cytochromes and are clearly present after correction for pseudocontact shifts in the oxidized form (Boyd J, Dobson CM, Morar AS, Williams RJP, Pielak GJ (1999) J Am Chem Soc 121:9247-9248; Guiles RD, Basus VJ, Sarma S, Malpure S, Fox KM, Kuntz ID, Waskell L (1993) Biochemistry 32:8329-8340). 15N-HSQC experiments have been performed on both oxidized and reduced forms of cytochrome b5 in the absence and in the presence of 2 M guanidinium chloride (GdmCl). GdmCl in this concentration is known to sizably alter the structure of the oxidized form of the protein and, in particular, to perturb the hydrogen bonding network. However, the perturbation of the 15N-NMR chemical shift changes is minor compared to the changes occurring upon reduction. It is concluded that changes in hydrogen bonding upon reduction must be modest and cannot account for the observed chemical shift effects. Alternative explanations should thus be looked for.     

Troglochaetus beranecki Delachaux (Annelida, Polychaeta): collecting methods and microscopy techniques for SEM and in vivo observations

The methods and the instruments for sampling and observation in vivo of the polychaete Troglochaetus beranecki are briefly described. Some SEM observations are reported. This revised version was published online in July 2006 with corrections to the Cover Date.     

Unfolding of beta‐lactoglobulin on the surface of polystyrene nanoparticles: Experimental and computational approaches

Structural changes ensuing from the non‐covalent absorption of bovine beta‐lactoglobulin (BLG) on the surface of polystyrene nanoparticles were investigated by using spectroscopic approaches, by assessing the reactivity of specific residues, and by limited proteolysis/mass spectrometry. Also, the immunoreactivity of absorbed and free BLG was compared. All these approaches indicated substantial rearrangements of the protein structure in the absorbed state, in spite of the reported structural rigidity of BLG. Changes made evident by experimental measurements were confirmed by computational approaches. These indicate that adsorption‐related changes are most marked in the area between the main C‐terminal alpha helix and the beta‐barrel, and lead to full exposure of the thiol on Cys₁₂₁, consistent with experimental measurements. In the computational model of bound BLG, both Trp₆₁ and Trp₁₉ also move away from their neighboring quenchers and become solvent‐exposed, as indicated by fluorescence measurement. Upon binding, the beta‐barrel also loosens, with a substantial increase in immunoreactivity and with noticeable changes in the trypsinolytic pattern. The possible general significance of the structural changes reported here for non‐covalently adsorbed BLG is discussed with respect to recognition events involving surface‐bound proteins, as are aspects related to the carrier function(s) of BLG, and to its use as a common ingredient in many food systems. Proteins 2014; 82:1272–1282. © 2013 Wiley Periodicals, Inc.     

Matrix metalloproteinase–inhibitor interaction: the solution structure of the catalytic domain of human matrix metalloproteinase-3 with different inhibitors

We structurally characterized the adducts of the catalytic domain of matrix metalloproteinase-3 (MMP3) with three different nonpeptidic inhibitors by solving the solution structure of one adduct [MMP3–N-isobutyl-N-(4-methoxyphenylsulfonyl)glycyl hydroxamic acid] and then by calculating structural models of the other two adducts using a reduced set of experimental NMR data, following a recently proposed procedure (Bertini et al. in J. Med. Chem. 48:7544–7559, 2005). The inhibitors were selected with the criteria of maintaining in all of them the same zinc-coordinating moiety and of selectively changing the substituents and/or the functional groups. The backbone dynamics on various time scales have been characterized as well. The comparison among these structures and with others previously reported allowed us to elucidate fine details of inhibitor–receptor interactions and to develop some criteria, which could guide in optimizing the design of selective inhibitors. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Daily Fluctuations of Antioxidants in Bean (Phaseolus vulgaris L.) Leaves As Affected by the Presence of Ambient Air Pollutants

During the period 0800–1700 h (GMT) of a summer day, youngleaves were collected every 20 min from Phaseolus vulgaris L.cv. Horticultural plants grown in open-top field chambers locatedat an urban site in northern Italy and exposed either to ambientlevels of gaseous air pollutants or to filtered ambient air.Ascorbic and dehydroascorbic acids, GSH and GSSG, superoxidedismutase, ascorbate peroxidase, dehydroascorbate reductase,GSSG reductase, GSH peroxidase, catalase, guaiacol peroxidase,chlorophylls, carotenoids, soluble protein and dry weight weremeasured in these leaves. The main differences between treatedand control leaves were observed during the period 1100–1530h and concerned superoxide dismutase, catalase, ascorbate peroxidase,ascorbate/dehydroascorbate and GSH/GSSG ratios, chlorophylls,carotenoids and dry weight. On the basis of the pollution climateobserved at the experimental site on the day of leaves sampling,ozone appeared to be the causative agent of the observed divergencesamong the time patterns of antioxidants in treated and controlplants. It was deduced that ozone can induce oxidative stressvia the production of superoxide radical anion and hydrogenperoxide. (Received June 1, 1992; Accepted December 9, 1992)     

H NOE studies of oxidized high potential iron sulfur protein II from Ectothiorhodospira halophila

The ¹H NMR spectra of oxidized HiPIP II from Ectothiorhodospira halophila have been recorded at 600 MHz. Nuclear Overhauser effect measurements have allowed the assignment of the cysteine β-CH₂ resonances. Four β-CH₂ signals are downfield shifted and four upfield shifted. Through a theoretical model and on the ground of Mössbauer data on analogous systems we propose that the upfield signals are those of the cysteines bound to the iron(III) ions and those downfield of the cysteines bound to the mixed valence pair Fe(III)-Fe(II).     

A novel aminopeptidase associated with the 60 kDa chaperonin in the thermophilic archaeon Sulfolobus solfataricus

The chaperonins are high-molecular-weight protein complexes having a characteristic double-ring toroidal shape; they are thought to aid the folding of denatured or newly synthesized polypeptides. These proteins exist as two functionally similar but distantly related families, one including the bacterial and organellar chaperonins and the other (termed the CCT-TRiC family) including the chaperonins of the Archaea and the eukaryotes. The CCT-TRiC chaperonins, particularly their archeal members, are less well known than their bacterial counterparts, and their main cellular function is still doubtful. In this work, we report that the chaperonin of the thermophilic archaeon Sulfolobus solfataricus interacts with several polypeptides other than the two subunits that constitute the 18-mer double-ring structure. We have cloned and sequenced the gene encoding one 90 kDa chaperonin-associated protein and have shown, using biochemical assays, that the product is an enzyme belonging to the family of zinc-dependent aminopeptidases. The Sulfolobus protein shows maximal homology to eukaryotic (yeast and mouse) aminopeptidases. It contains a leucine zipper motif and can be phosphorylated by an unidentified kinase present in the cell extracts. The possible significance of an association between an aminopeptidase and a chaperonin is discussed.